DOCSLIB.ORG

Full Book Final

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Full Book Final WELCOME ! On behalf of the ECCB10 Organizing and Steering Committees we would like to welcome you to beautiful Ghent, one of Europe’s most exciting cities. We hope you will enjoy ECCB10 - four days of presentations, poster sessions, workshops, software demonstrations and networking with other leading bioinformatics researchers, computational biologists and bio-IT professionals from around the world. ECCB is the leading European meeting in our field and a primary international conference at which people present and discuss advances in computational biology. We are proud to have five keynote lectures by distinguished speakers Peer Bork (European Molecular Biology Laboratory, Heidelberg, Germany), Elaine Mardis (Washington University Genome Center, St-Louis, MO, USA), Michael J. E. Sternberg (Imperial College, London, UK), Yves Van de Peer (Flemish Institute of Biotechnology and University of Ghent, Belgium) and Hans Westerhoff (University of Manchester, UK and VU University Amsterdam, The Netherlands). In addition, there will be a number of interesting workshops and tutorials on Sunday, including the first European Student Council Symposium, a workshop on leveraging perturbation effects towards reverse engineering biological networks and one on extraction and reuse of genotype-phenotype knowledge from scientific literature and databases. There is no better way to kick off ECCB10 than to participate in one of these workshops and tutorials! On Monday afternoon, we will have a special joint lecture by artist Koen Vanmechelen and geneticist Jean- Jacques Cassiman. They will present the Cosmopolitan Chicken Project – Koen’s quest to create a universal, cosmopolitan chicken. Further, they will discuss how art and science influence each other. We would like to acknowledge the help of all people who made ECCB10 happen, as well as our commercial and academic sponsors – thanks to them we were able to offer 62 fellowships for early-stage scientists. Finally, we would like to thank you for your participation. Enjoy the conference! Yves Moreau & Jaap Heringa ECCB10 Table of Contents TABLE OF CONTENTS Hotels ...................................................................................................................................................................... 4 Local Public Transport ........................................................................................................................................... 5 Floor Plan ............................................................................................................................................................... 6 Organization ........................................................................................................................................................... 7 Keynotes ............................................................................................................................................................... 15 Schedule ............................................................................................................................................................... 17 Social Events ........................................................................................................................................................ 25 Workshops ............................................................................................................................................................ 26 Tutorials ................................................................................................................................................................ 29 Art Meets Science ................................................................................................................................................. 34 Technology Track ................................................................................................................................................. 35 Oral Presentations ................................................................................................................................................. 45 Posters .................................................................................................................................................................. 61 Author Index ....................................................................................................................................................... 102 3 ECCB10 Hotels HOTELS NH Gent Sint Pieters Hotel Novotel Gent Centrum Koning Albertlaan 121, 9000 Ghent, Belgium Goudenleeuwplein 5, 9000 Ghent, Belgium +32 9 222 60 65 +32 9 224 22 30 Holiday Inn Gent Expo Carlton Hotel Gent Maaltekouter 3, 9051 Ghent, Belgium Koningin Astridlaan 138, 9000 Ghent, Belgium +32 9 220 24 24 +32 9 222 88 36 NH Gent Belfort Hostel 47 Hoogpoort 63, 9000 Ghent, Belgium Blekerijstraat 47, 9000 Ghent, Belgium +32 9 233 33 31 +32 478 71 28 27 Ghent Marriott Hotel HI De Draecke Gent Korenlei 10, 9000 Ghent, Belgium Sint-Widostraat 11, 9000 Ghent, Belgium +32 9 233 93 93 +32 9 233 70 50 Hotel Gravensteen Ecohostel Andromeda Jan Breydelstraat 35, 9000 Ghent, Belgium Bargiekaai 35, 9000 Ghent, Belgium +32 9 225 11 50 +32 486 67 80 33 Ghent River Hotel Waaistraat 5, 9000 Ghent, Belgium +32 9 266 10 10 Hotel de Flandre Poel 1, 9000 Ghent, Belgium +32 9 266 06 00 Hotel Ibis Gent Centrum Opera Nederkouter 24-26, 9000 Ghent, Belgium +32 9 225 07 07 Hotel Ibis Centrum St-Baafs Kathedraal Limburgstraat 2, 9000 Ghent, Belgium +32 9 233 00 00 Holiday Inn Gent Express Akkerhage 2, 9000 Ghent, Belgium +32 9 222 58 85 Campanile Akkerhage 1, 9000 Ghent, Belgium +32 9 220 02 22 Poortackere Monasterium Oude Houtlei 58, 9000 Ghent, Belgium +32 9 269 22 30 4 ECCB10 Local Public Transport LOCAL PUBLIC TRANSPORT Basics ‘De Lijn’ (http://www.delijn.be) provides trams and buses in Ghent. Using public transport is easy and travelers are offered several ticket options, but in any case buying your ticket in one of the distribution points (train station, kiosks, supermarkets…) is at least 25% cheaper than buying it from the bus or tram driver. If you are considering taking several bus/tram trips you might be interested in the “lijnkaart”, which grants the owner 10 trips at a discount rate. People traveling in groups of 5 or more can buy a “lijnkaart %” which also provides 10 trips at an even lower rate. If you plan on using public transportation a lot, a day-pass or a 3-day-pass might be the most convenient way of traveling through Ghent. Once you have bought a ticket traveling is as simple as getting on the bus, saying “Goeiedag!” to the driver and inserting the ticket into the yellow validation device (don’t forget to take it back). Transfers are allowed for one hour after validation. Ticket Type Price at distribution point Price on the bus/tram Single ticket € 1,20 € 2 Lijnkaart (10 trips) € 8 € 15 Lijnkaart % (10 trips) € 6 € 11 Day-pass € 5 € 6 3-day-pass € 10 € 12 Museum Pass (3-day-pass, includes access to the city’s museums): € 20 From the conference site to the city centre Bus 5 is a convenient way to go to the city centre. It leaves from the bus stop in front of the conference site. You will find a map of public transport in the conference bag. Ghent Museum Pass The Ghent Museum Pass costs € 20 and offers access to various museums and municipal buildings for 3 days. During those 3 days the Ghent Museum Pass is also valid as a ticket for all De Lijn vehicles in the Ghent city area. The validity period starts on the date that you write on the back of the pass. You can purchase a Ghent Museum Pass in advance and use it for your journey to the first museum. You can purchase the Ghent Museum Pass in the Lijnwinkels in East Flanders, in participating museums, from the tourism department of the city of Ghent, and in several Ghent hotels. The participating museums and municipal buildings are: Belfry, Friary of the Carmelites, Design Museum Ghent, De wereld van Kina: the Garden, De wereld van Kina: the House, The Castle of the Counts, Alijn House, Art Centre St Peter’s Abbey, MIAT (Museum for Industrial Archaeology and Textiles), Museum Dr. Guislain, Museum for the History of the Sciences, Museum of Fine Arts, St Bavo's Cathedral + The Adoration of the Mystic Lamb, SMAK (City Museum for Modern Art), STAM (City Museum Ghent). More information available at De Lijn's website (http://www.delijn.be/en/vervoerbewijzen/types/uitstap/#5). 5 ECCB10 Floor Plan FLOOR PLAN 6 ECCB10 Organization ORGANIZATION Conference Chair Yves Moreau, Katholieke Universiteit Leuven, Belgium Proceedings Chair Jaap Heringa, VU University Amsterdam, The Netherlands Local Organizing Committee Yves Moreau, Katholieke Universiteit Leuven, Belgium Jaap Heringa, VU University Amsterdam, The Netherlands Gert Vriend, Radboud University, Nijmegen, The Netherlands Yves Van de Peer, University of Ghent and VIB, Belgium Kathleen Marchal, Katholieke Universiteit Leuven, Belgium Jacques van Helden, Université Libre de Bruxelles, Belgium Louis Wehenkel, Université de Liège, Belgium Antoine van Kampen, University of Amsterdam and Netherlands Bioinformatics Center (NBIC) Peter van der Spek, Erasmus MC, Rotterdam, The Netherlands Steering Committee Michal Linial (Chair), Hebrew University, Jerusalem, Israel Soren Brunak, Technical University of Denmark, Lyngby, Denmark Philipp Bucher, University of Lausanne, Switzerland David Gilbert, University of Glasgow, UK Thomas Lengauer, Max-Planck Institute for Informatics, Saarbrücken, Germany Yves Moreau,
Load more

Recommended publications
  • Predicting and Characterising Protein-Protein Complexes
    Predicting and Characterising Protein-Protein Complexes Iain Hervé Moal June 2011 Biomolecular Modelling Laboratory, Cancer Research UK London Research Institute and Department of Biochemistry and Molecular Biology, University College London A thesis submitted in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Biochemistry at the University College London. 2 I, Iain Hervé Moal, confirm that the work presented in this thesis is my own. Where information has been derived from other sources, I confirm that this has been indicated in the thesis. Abstract Macromolecular interactions play a key role in all life processes. The con- struction and annotation of protein interaction networks is pivotal for the understanding of these processes, and how their perturbation leads to dis- ease. However the extent of the human interactome and the limitations of the experimental techniques which can be brought to bear upon it necessit- ate theoretical approaches. Presented here are computational investigations into the interactions between biological macromolecules, focusing on the structural prediction of interactions, docking, and their kinetic and thermo- dynamic characterisation via empirical functions. Firstly, the use of normal modes in docking is investigated. Vibrational analysis of proteins are shown to indicate the motions which proteins are intrinsically disposed to under- take, and the use of this information to model flexible deformations upon protein-protein binding is evaluated. Subsequently SwarmDock, a docking algorithm which models flexibility as a linear combination of normal modes, is presented and benchmarked on a wide variety of test cases. This algorithm utilises state of the art energy functions and metaheuristics to navigate the free energy landscape.
    [Show full text]
  • Functional Effects Detailed Research Plan
    GeCIP Detailed Research Plan Form Background The Genomics England Clinical Interpretation Partnership (GeCIP) brings together researchers, clinicians and trainees from both academia and the NHS to analyse, refine and make new discoveries from the data from the 100,000 Genomes Project. The aims of the partnerships are: 1. To optimise: • clinical data and sample collection • clinical reporting • data validation and interpretation. 2. To improve understanding of the implications of genomic findings and improve the accuracy and reliability of information fed back to patients. To add to knowledge of the genetic basis of disease. 3. To provide a sustainable thriving training environment. The initial wave of GeCIP domains was announced in June 2015 following a first round of applications in January 2015. On the 18th June 2015 we invited the inaugurated GeCIP domains to develop more detailed research plans working closely with Genomics England. These will be used to ensure that the plans are complimentary and add real value across the GeCIP portfolio and address the aims and objectives of the 100,000 Genomes Project. They will be shared with the MRC, Wellcome Trust, NIHR and Cancer Research UK as existing members of the GeCIP Board to give advance warning and manage funding requests to maximise the funds available to each domain. However, formal applications will then be required to be submitted to individual funders. They will allow Genomics England to plan shared core analyses and the required research and computing infrastructure to support the proposed research. They will also form the basis of assessment by the Project’s Access Review Committee, to permit access to data.
    [Show full text]
  • Development of Novel Strategies for Template-Based Protein Structure Prediction
    Imperial College London Department of Life Sciences PhD Thesis Development of novel strategies for template-based protein structure prediction Stefans Mezulis supervised by Prof. Michael Sternberg Prof. William Knottenbelt September 2016 Abstract The most successful methods for predicting the structure of a protein from its sequence rely on identifying homologous sequences with a known struc- ture and building a model from these structures. A key component of these homology modelling pipelines is a model combination method, responsible for combining homologous structures into a coherent whole. Presented in this thesis is poing2, a model combination method using physics-, knowledge- and template-based constraints to assemble proteins us- ing information from known structures. By combining intrinsic bond length, angle and torsional constraints with long- and short-range information ex- tracted from template structures, poing2 assembles simplified protein models using molecular dynamics algorithms. Compared to the widely-used model combination tool MODELLER, poing2 is able to assemble models of ap- proximately equal quality. When supplied only with poor quality templates or templates that do not cover the majority of the query sequence, poing2 significantly outperforms MODELLER. Additionally presented in this work is PhyreStorm, a tool for quickly and accurately aligning the three-dimensional structure of a query protein with the Protein Data Bank (PDB). The PhyreStorm web server provides comprehensive, current and rapid structural comparisons to the protein data bank, providing researchers with another tool from which a range of biological insights may be drawn. By partitioning the PDB into clusters of similar structures and performing an initial alignment to the representatives of each cluster, PhyreStorm is able to quickly determine which structures should be excluded from the alignment.
    [Show full text]
  • 120421-24Recombschedule FINAL.Xlsx
    Friday 20 April 18:00 20:00 REGISTRATION OPENS in Fira Palace 20:00 21:30 WELCOME RECEPTION in CaixaForum (access map) Saturday 21 April 8:00 8:50 REGISTRATION 8:50 9:00 Opening Remarks (Roderic GUIGÓ and Benny CHOR) Session 1. Chair: Roderic GUIGÓ (CRG, Barcelona ES) 9:00 10:00 Richard DURBIN The Wellcome Trust Sanger Institute, Hinxton UK "Computational analysis of population genome sequencing data" 10:00 10:20 44 Yaw-Ling Lin, Charles Ward and Steven Skiena Synthetic Sequence Design for Signal Location Search 10:20 10:40 62 Kai Song, Jie Ren, Zhiyuan Zhai, Xuemei Liu, Minghua Deng and Fengzhu Sun Alignment-Free Sequence Comparison Based on Next Generation Sequencing Reads 10:40 11:00 178 Yang Li, Hong-Mei Li, Paul Burns, Mark Borodovsky, Gene Robinson and Jian Ma TrueSight: Self-training Algorithm for Splice Junction Detection using RNA-seq 11:00 11:30 coffee break Session 2. Chair: Bonnie BERGER (MIT, Cambrige US) 11:30 11:50 139 Son Pham, Dmitry Antipov, Alexander Sirotkin, Glenn Tesler, Pavel Pevzner and Max Alekseyev PATH-SETS: A Novel Approach for Comprehensive Utilization of Mate-Pairs in Genome Assembly 11:50 12:10 171 Yan Huang, Yin Hu and Jinze Liu A Robust Method for Transcript Quantification with RNA-seq Data 12:10 12:30 120 Zhanyong Wang, Farhad Hormozdiari, Wen-Yun Yang, Eran Halperin and Eleazar Eskin CNVeM: Copy Number Variation detection Using Uncertainty of Read Mapping 12:30 12:50 205 Dmitri Pervouchine Evidence for widespread association of mammalian splicing and conserved long range RNA structures 12:50 13:10 169 Melissa Gymrek, David Golan, Saharon Rosset and Yaniv Erlich lobSTR: A Novel Pipeline for Short Tandem Repeats Profiling in Personal Genomes 13:10 13:30 217 Rory Stark Differential oestrogen receptor binding is associated with clinical outcome in breast cancer 13:30 15:00 lunch break Session 3.
    [Show full text]
  • Python for Bioinformatics, Second Edition
    PYTHON FOR BIOINFORMATICS SECOND EDITION CHAPMAN & HALL/CRC Mathematical and Computational Biology Series Aims and scope: This series aims to capture new developments and summarize what is known over the entire spectrum of mathematical and computational biology and medicine. It seeks to encourage the integration of mathematical, statistical, and computational methods into biology by publishing a broad range of textbooks, reference works, and handbooks. The titles included in the series are meant to appeal to students, researchers, and professionals in the mathematical, statistical and computational sciences, fundamental biology and bioengineering, as well as interdisciplinary researchers involved in the field. The inclusion of concrete examples and applications, and programming techniques and examples, is highly encouraged. Series Editors N. F. Britton Department of Mathematical Sciences University of Bath Xihong Lin Department of Biostatistics Harvard University Nicola Mulder University of Cape Town South Africa Maria Victoria Schneider European Bioinformatics Institute Mona Singh Department of Computer Science Princeton University Anna Tramontano Department of Physics University of Rome La Sapienza Proposals for the series should be submitted to one of the series editors above or directly to: CRC Press, Taylor & Francis Group 3 Park Square, Milton Park Abingdon, Oxfordshire OX14 4RN UK Published Titles An Introduction to Systems Biology: Statistical Methods for QTL Mapping Design Principles of Biological Circuits Zehua Chen Uri Alon
    [Show full text]
  • Centre for Bioinformatics Imperial College London
    Centre for Bioinformatics Imperial College London Inaugural Report January 2003 Centre Director: Prof Michael Sternberg www.imperial.ac.uk/bioinformatics [email protected] Support Service Head: Dr Sarah Butcher www.codon.bioinformatics.ic.ac.uk [email protected] Centre for Bioinformatics - Imperial College London - Inaugural Report - January 2003 1 Contents Summary..................................................................................................................... 3 1. Background and Objectives .................................................................................... 4 1.1 Background ....................................................................................................... 4 1.2 Objectives of the Centre for Bioinformatics ....................................................... 4 1.3 Objectives of the Bioinformatics Support Service.............................................. 5 1.4 Historical Notes ................................................................................................. 5 2. Management ........................................................................................................... 6 3. Biographies of the Team......................................................................................... 7 4. Bioinformatics Research at Imperial ....................................................................... 8 4.1 Affiliates of the Centre ....................................................................................... 8 4.2 Research Grants
    [Show full text]
  • Centre for Bioinformatics Imperial College London Second Report 31
    Centre for Bioinformatics Imperial College London Second Report 31 May 2004 Centre Director: Prof Michael Sternberg www.imperial.ac.uk/bioinformatics [email protected] Support Service Head: Dr Sarah Butcher www.codon.bioinformatics.ic.ac.uk [email protected] Centre for Bioinformatics - Imperial College London - Second Report - May 2004 1 Contents Summary..................................................................................................................... 3 1. Background and Objectives .................................................................................. 4 1.1 Objectives of the Report........................................................................................ 4 1.2 Background........................................................................................................... 4 1.3 Objectives of the Centre for Bioinformatics........................................................... 5 1.4 Objectives of the Bioinformatics Support Service ................................................. 5 2. Management ......................................................................................................... 6 3. Biographies of the Team....................................................................................... 7 4. Bioinformatics Research at Imperial ..................................................................... 8 4.1 Affiliates of the Centre........................................................................................... 8 4.2 Research..............................................................................................................
    [Show full text]
  • F. Alex Feltus, Ph.D
    F. Alex Feltus, Ph.D. Curriculum Vitae 001010101000001000100001011001010101001000101001010010000100001010101001001000010010001000100001010001001010100100010001000101001000011110101000110010100010101010101010110101010100001000010010101010100100100000101001010010001010110100010 Clemson University • Department of Genetics & Biochemistry Biosystems Research Complex Rm 302C • 105 Collings St. • Clemson, SC 29634 (864)656-3231 (office) • (864) 654-5403 (home) • Skype: alex.feltus • [email protected] https://www.clemson.edu/science/departments/genetics-biochemistry/people/profiles/ffeltus https://orcid.org/0000-0002-2123-6114 https://www.linkedin.com/in/alex-feltus-86a0073a 001010101000001010101010101010101010100110000101100101010100100010100101001000010000101010100100100001001000100010000101000100101010010001000100010100100001111010100011001010001000001000010010101010100100100000101001010010001010110100010 Educational Background: Ph.D. Cell Biology (2000) Vanderbilt University (Nashville, TN) B.Sc. Biochemistry (1992) Auburn University (Auburn, AL) Ph.D. Dissertation Title: Transcriptional Regulation of Human Type II 3β-Hydroxysteroid Dehydrogenase: Stat5- Centered Control by Steroids, Prolactin, EGF, and IL-4 Hormones. Professional Experience: 2018- Professor, Clemson University Department of Genetics and Biochemistry 2017- Core Faculty, Biomedical Data Science and Informatics (BDSI) PhD Program 2018- Faculty Member, Clemson Center for Human Genetics 2020- Faculty Scholar, Clemson University School of Health Research (CUSHR) 2019- co-Founder,
    [Show full text]
  • ACM-BCB 2016 the 7Th ACM Conference on Bioinformatics
    ACM-BCB 2016 The 7th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics October 2-5, 2016 Organizing Committee General Chairs: Steering Committee: Ümit V. Çatalyürek, Georgia Institute of Technology Aidong Zhang, State University of NeW York at Buffalo, Genevieve Melton-Meaux, University of Minnesota Co-Chair May D. Wang, Georgia Institute of Technology and Program Chairs: Emory University, Co-Chair John Kececioglu, University of Arizona Srinivas Aluru, Georgia Institute of Technology Adam Wilcox, University of Washington Tamer Kahveci, University of Florida Christopher C. Yang, Drexel University Workshop Chair: Ananth Kalyanaraman, Washington State University Tutorial Chair: Mehmet Koyuturk, Case Western Reserve University Demo and Exhibit Chair: Robert (Bob) Cottingham, Oak Ridge National Laboratory Poster Chairs: Lin Yang, University of Florida Dongxiao Zhu, Wayne State University Registration Chair: Preetam Ghosh, Virginia CommonWealth University Publicity Chairs Daniel Capurro, Pontificia Univ. Católica de Chile A. Ercument Cicek, Bilkent University Pierangelo Veltri, U. Magna Graecia of Catanzaro Student Travel Award Chairs May D. Wang, Georgia Institute of Technology and Emory University JaroslaW Zola, University at Buffalo, The State University of NeW York Student Activity Chair Marzieh Ayati, Case Western Reserve University Dan DeBlasio, Carnegie Mellon University Proceedings Chairs: Xinghua Mindy Shi, U of North Carolina at Charlotte Yang Shen, Texas A&M University Web Admins: Anas Abu-Doleh, The
    [Show full text]
  • Spinout Equinox Pharma Speeds up and Reduces the Cost of Drug Discovery
    Spinout Equinox Pharma speeds up and reduces the cost of drug discovery pinout Equinox Pharma1 provides a service to the pharma and biopharma industries that helps in the development of new drugs. The company, established by researchers from Imperial College London in IMPACT SUMMARY 2008, is using its own proprietary software to help speed up and reduce the cost of discovery processes. S Spinout Equinox Pharma provides services to the agri- tech and pharmaceuticals industries to accelerate the Equinox is based on BBSRC-funded collaborative research The technology also has applications in the agrochemical discovery of molecules that could form the basis of new conducted by Professors Stephen Muggleton2, Royal sector, and is being used by global agri-tech company products such as drugs or herbicides. Academy Chair in Machine Learning, Mike Sternberg3, Chair Syngenta. The company arose from BBSRC bioinformatics and of Structural Bioinformatics, and Paul Freemont4, Chair of structural biology research at Imperial College London. Protein Crystallography, at Imperial College London. “The power of a logic-based approach is that it can Technology commercialisation company NetScientific propose chemically-novel molecules that can have Ltd has invested £250K in Equinox. The technology developed by the company takes a logic- enhanced properties and are able to be the subject of novel Equinox customers include major pharmaceutical based approach to discover novel drugs, using computers to ‘composition of matter’ patents,” says Muggleton. companies such as Japanese pharmaceutical company learn from a set of biologically-active molecules. It combines Astellas and agro chemical companies such as knowledge about traditional drug discovery methods and Proving the technology Syngenta, as well as SMEs based in the UK, Europe, computer-based analyses, and focuses on the key stages in A three-year BBSRC grant in 2003 funded the work of Japan and the USA.
    [Show full text]
  • Optical Maps in Guided Genome Assembly
    Optical maps in guided genome assembly Miika Leinonen Helsinki September 9, 2019 UNIVERSITY OF HELSINKI Master’s Programme in Computer Science HELSINGIN YLIOPISTO — HELSINGFORS UNIVERSITET — UNIVERSITY OF HELSINKI Tiedekunta — Fakultet — Faculty Koulutusohjelma — Studieprogram — Study Programme Faculty of Science Study Programme in Computer Science Tekijä — Författare — Author Miika Leinonen Työn nimi — Arbetets titel — Title Optical maps in guided genome assembly Ohjaajat — Handledare — Supervisors Leena Salmela and Veli Mäkinen Työn laji — Arbetets art — Level Aika — Datum — Month and year Sivumäärä — Sidoantal — Number of pages Master’s thesis September 9, 2019 41 pages + 0 appendices Tiivistelmä — Referat — Abstract With the introduction of DNA sequencing over 40 years ago, we have been able to take a peek at our genetic material. Even though we have had a long time to develop sequencing strategies further, we are still unable to read the whole genome in one go. Instead, we are able to gather smaller pieces of the genetic material, which we can then use to reconstruct the original genome with a process called genome assembly. As a result of the genome assembly we often obtain multiple long sequences representing different regions of the genome, which are called contigs. Even though a genome often consists of a few separate DNA molecules (chromosomes), the number of obtained contigs outnumbers them substantially, meaning our reconstruction of the genome is not perfect. The resulting contigs can afterwards be refined by ordering, orienting and scaffolding them using additional information about the genome, which is often done manually by hand. The assembly process can also be guided automatically with the additional information, and in this thesis we are introducing a method that utilizes optical maps to aid us assemble the genome more accurately.
    [Show full text]
  • ISBRA 2012 Short Abstracts
    1 ISBRA 20 2 SHORT ABSTRACTS 8TH INTERNATIONAL SYMPOSIUM ON BIOINFORMATICS RESEARCH AND APPLICATIONS May 21-23, 2012 University of Texas at Dallas, Dallas, TX http://www.cs.gsu.edu/isbra12/ Symposium Organizers Steering Committee Dan Gusfield, University of California, Davis Ion Mandoiu, University of Connecticutt Yi Pan, Georgia State University Marie-France Sagot, INRIA Alex Zelikovsky, Georgia State University General Chairs Ovidiu Daesku, University of Texas at Dallas Raj Sunderraman, Georgia State University Program Chairs Leonidas Bleris, University of Texas at Dallas Ion Mandoiu, University of Connecticut Russell Schwartz, Carnegie Mellon University Jianxin Wang, Central South University Publicity Chair Sahar Al Seesi, University of Connecticut Finance Chairs Anu Bourgeois, Georgia State University Raj Sunderraman, Georgia State University Web Master, Web Design Piyaphol Phoungphol J. Steven Kirtzic Sponsors NATIONAL SCIENCE DEPARTMENT OF COMPUTER SCIENCE DEPARTMENT OF COMPUTER SCIENCE FOUNDATION GEORGIA STATE UNIVESITY UNIVERSITY OF TEXAS AT DALLAS i Program Committee Members Srinivas Aluru, Iowa State University Allen Holder, Rose-Hulman Istitute of S. Cenk Sahinalp, Simon Fraser Danny Barash, Ben-Gurion Technology University University Jinling Huang, Eastern Carolina David Sankoff, University of Ottawa Robert Beiko, Dalhousie University University Russell Schwartz, Carnegie Mellon Anne Bergeron, Universite du Lars Kaderali, University of University Quebec a Montreal Heidelberg Joao Setubal, Virginia Bioinformatics Iyad Kanj,
    [Show full text]